Single cell UOW (excluding Slide TS36)

Intensities of Differentially Expressed Markers for Stem cells condition

Project description: Initial datasets shared by Australian collaborators (Tassiani Sarretto, Helena Anastacio). Three conditions (stem cells, cells grown for 7 and 14 days). 12 replicates per condition. One slide (TS36) including cells grown 7 days was excluded from this analysis (possible batch effects...?)

Date: 2023-05-30

Config: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/plots_without_TS36/config_QC_stem.yml

Notebook version: v0.2.0.post3+g966cb55.d20230408 (git-commit: 9f02807)

Report parameters

  • Biological key: growthConditions
  • Slide key: slide
  • Process slides independently: False
  • Replicate key: replicate_nb_overall
  • Masking key: None
  • AnnData pattern: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/anndatas/{slide}-well{well}-{row}{col}.h5ad
  • AnnData type: AnnDatas downloaded from Metaspace
  • Metadata file path: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/metadata_mod_full.csv
Links to ion images for selected markers
  Slide TS33 Slide TS34 Slide TS35 Slide TS36 Slide TS37 Slide TS38
Marker formula            
TIC TIC TIC TIC TIC TIC TIC
C16H18O6+Na 2-[2-hydroxy-3-(3-hydroxy... 2-[2-hydroxy-3-(3-hydroxy... 2-[2-hydroxy-3-(3-hydroxy... 2-[2-hydroxy-3-(3-hydroxy... 2-[2-hydroxy-3-(3-hydroxy... 2-[2-hydroxy-3-(3-hydroxy...
C25H47O8P+NH4 PA(2:0/20:1(11Z)) PA(2:0/20:1(11Z)) PA(2:0/20:1(11Z)) PA(2:0/20:1(11Z)) PA(2:0/20:1(11Z)) PA(2:0/20:1(11Z))
C25H50NO8P+H PC(2:0/15:0) PC(2:0/15:0) PC(2:0/15:0) PC(2:0/15:0) PC(2:0/15:0) PC(2:0/15:0)
C30H45NO5+Na Hydroxybuprenorphine Hydroxybuprenorphine Hydroxybuprenorphine Hydroxybuprenorphine Hydroxybuprenorphine Hydroxybuprenorphine
C38H75O7P+NH4 PA(O-13:0/22:1(13Z)) PA(O-13:0/22:1(13Z)) PA(O-13:0/22:1(13Z)) PA(O-13:0/22:1(13Z)) PA(O-13:0/22:1(13Z)) PA(O-13:0/22:1(13Z))
C38H78NO7P+H PC(0:0/30:0) PC(0:0/30:0) PC(0:0/30:0) PC(0:0/30:0) PC(0:0/30:0) PC(0:0/30:0)
C39H78NO6P+NH4 CerP(d18:1(4E)/21:0) CerP(d18:1(4E)/21:0) CerP(d18:1(4E)/21:0) CerP(d18:1(4E)/21:0) CerP(d18:1(4E)/21:0) CerP(d18:1(4E)/21:0)
C39H81N2O6P+H N-hexadecanoylsphinganine... N-hexadecanoylsphinganine... N-hexadecanoylsphinganine... N-hexadecanoylsphinganine... N-hexadecanoylsphinganine... N-hexadecanoylsphinganine...
C42H81O10P+NH4 Lysobisphosphatidate (10:... Lysobisphosphatidate (10:... Lysobisphosphatidate (10:... Lysobisphosphatidate (10:... Lysobisphosphatidate (10:... Lysobisphosphatidate (10:...
C42H82NO11P+Na IPC(d18:0/18:1(9Z)) IPC(d18:0/18:1(9Z)) IPC(d18:0/18:1(9Z)) IPC(d18:0/18:1(9Z)) IPC(d18:0/18:1(9Z)) IPC(d18:0/18:1(9Z))
C42H83O7P+NH4 PA(O-13:0/26:1(17Z)) PA(O-13:0/26:1(17Z)) PA(O-13:0/26:1(17Z)) PA(O-13:0/26:1(17Z)) PA(O-13:0/26:1(17Z)) PA(O-13:0/26:1(17Z))
C42H84NO8P+Na PC(4:0/30:0) PC(4:0/30:0) PC(4:0/30:0) annotation_id C42H84NO8P+Na PC(4:0/30:0) C42H84NO8P+Na PC(14:0/20:0) Name: molecule_name, dtype: object PC(4:0/30:0) PC(4:0/30:0)
C42H86NO7P+H PC(O-13:0/21:0) PC(O-13:0/21:0) PC(O-13:0/21:0) PC(O-13:0/21:0) PC(O-13:0/21:0) PC(O-13:0/21:0)
C43H75NO4+Na Cer(iso-t17:0/26:6(8Z,11Z... Cer(iso-t17:0/26:6(8Z,11Z... Cer(iso-t17:0/26:6(8Z,11Z... Cer(iso-t17:0/26:6(8Z,11Z... Cer(iso-t17:0/26:6(8Z,11Z... Cer(iso-t17:0/26:6(8Z,11Z...
C47H83NO4+Na Cer(iso-t17:0/30:6(12Z,15... Cer(iso-t17:0/30:6(12Z,15... Cer(iso-t17:0/30:6(12Z,15... Cer(iso-t17:0/30:6(12Z,15... Cer(iso-t17:0/30:6(12Z,15... Cer(iso-t17:0/30:6(12Z,15...

Ion Images for DE Markers

Annotation done at FDR 50% against the following databases: HMDB v4, SwissLipids 2018-02-02, KEGG v1

Ion images with TIC normalization: True

TIC

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (TIC)

Slide TS34 (TIC)

Slide TS35 (TIC)

Slide TS36 (TIC)

Slide TS37 (TIC)

Slide TS38 (TIC)

C16H18O6+Na

2-[2-hydroxy-3-(3-hydroxy-4-methoxyphenyl)propyl]benzene-1,3,5-triol, 2-[2-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propyl]benzene-1,3,5-triol, 6-O-Desmethyl-mycophenolic acid, trans-O-Methylgrandmarin

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C16H18O6+Na)

Slide TS34 (C16H18O6+Na)

Slide TS35 (C16H18O6+Na)

Slide TS36 (C16H18O6+Na)

Slide TS37 (C16H18O6+Na)

Slide TS38 (C16H18O6+Na)

C25H47O8P+NH4

PA(2:0/20:1(11Z)), PA(4:0/18:1(6Z)), PA(4:0/18:1(9Z)), PA(4:0/18:1(11E)), PA(4:0/18:1(11Z)), PA(6:0/16:1(6Z)), PA(6:0/16:1(9Z)), PA(8:0/14:1(9Z)), PA(14:1(9Z)/8:0), PA(16:1(6Z)/6:0), PA(16:1(9Z)/6:0), PA(18:1(6Z)/4:0), PA(18:1(9Z)/4:0), PA(18:1(11E)/4:0), PA(18:1(11Z)/4:0), PA(20:1(11Z)/2:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C25H47O8P+NH4)

Slide TS34 (C25H47O8P+NH4)

Slide TS35 (C25H47O8P+NH4)

Slide TS36 (C25H47O8P+NH4)

Slide TS37 (C25H47O8P+NH4)

Slide TS38 (C25H47O8P+NH4)

C25H50NO8P+H

PC(2:0/15:0), PC(3:0/14:0), PC(4:0/13:0), PC(13:0/4:0), PC(14:0/3:0), PC(15:0/2:0), PE(2:0/18:0), PE(3:0/17:0), PE(4:0/16:0), PE(6:0/14:0), PE(8:0/12:0), PE(10:0/10:0), PE(12:0/8:0), PE(14:0/6:0), PE(16:0/4:0), PE(17:0/3:0), PE(18:0/2:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C25H50NO8P+H)

Slide TS34 (C25H50NO8P+H)

Slide TS35 (C25H50NO8P+H)

Slide TS36 (C25H50NO8P+H)

Slide TS37 (C25H50NO8P+H)

Slide TS38 (C25H50NO8P+H)

C30H45NO5+Na

Hydroxybuprenorphine

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C30H45NO5+Na)

Slide TS34 (C30H45NO5+Na)

Slide TS35 (C30H45NO5+Na)

Slide TS36 (C30H45NO5+Na)

Slide TS37 (C30H45NO5+Na)

Slide TS38 (C30H45NO5+Na)

C38H75O7P+NH4

PA(O-13:0/22:1(13Z)), PA(O-15:0/20:1(11Z)), PA(O-17:0/18:1(6Z)), PA(O-17:0/18:1(9Z)), PA(O-17:0/18:1(11E)), PA(O-17:0/18:1(11Z)), PA(O-18:1(9Z)/17:0), PA(O-18:1(11Z)/17:0), PA(O-18:1(13Z)/17:0), PA(O-20:1(11Z)/15:0), PA(O-22:1(13Z)/13:0), PA(P-13:0/22:0), PA(P-14:0/21:0), PA(P-15:0/20:0), PA(P-16:0/19:0), PA(P-17:0/18:0), PA(P-18:0/17:0), PA(P-20:0/15:0), PA(P-22:0/13:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C38H75O7P+NH4)

Slide TS34 (C38H75O7P+NH4)

Slide TS35 (C38H75O7P+NH4)

Slide TS36 (C38H75O7P+NH4)

Slide TS37 (C38H75O7P+NH4)

Slide TS38 (C38H75O7P+NH4)

C38H78NO7P+H

PC(0:0/30:0), PC(30:0/0:0), PC(O-13:0/17:0), PC(O-14:0/16:0), PC(O-15:0/15:0), PC(O-16:0/14:0), PC(O-17:0/13:0), PC(O-18:0/12:0), PC(O-20:0/10:0), PC(O-22:0/8:0), PC(O-24:0/6:0), PC(O-26:0/4:0), PC(O-28:0/2:0), PC(o-14:0/16:0), PE(O-13:0/20:0), PE(O-14:0/19:0), PE(O-15:0/18:0), PE(O-16:0/17:0), PE(O-17:0/16:0), PE(O-18:0/15:0), PE(O-20:0/13:0), PE(O-30:0/3:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C38H78NO7P+H)

Slide TS34 (C38H78NO7P+H)

Slide TS35 (C38H78NO7P+H)

Slide TS36 (C38H78NO7P+H)

Slide TS37 (C38H78NO7P+H)

Slide TS38 (C38H78NO7P+H)

C39H78NO6P+NH4

CerP(d18:1(4E)/21:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C39H78NO6P+NH4)

Slide TS34 (C39H78NO6P+NH4)

Slide TS35 (C39H78NO6P+NH4)

Slide TS36 (C39H78NO6P+NH4)

Slide TS37 (C39H78NO6P+NH4)

Slide TS38 (C39H78NO6P+NH4)

C39H81N2O6P+H

N-hexadecanoylsphinganine-1-phosphocholine, PE-Cer(d14:0/23:0), PE-Cer(d16:0/21:0), PE-Cer(d18:0/19:0), PE-Cer(d20:0/17:0), SM(d14:0/20:0), SM(d16:0/18:0), SM(d18:0/16:0), SM(d20:0/14:0), SM(iso-d17:0/17:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C39H81N2O6P+H)

Slide TS34 (C39H81N2O6P+H)

Slide TS35 (C39H81N2O6P+H)

Slide TS36 (C39H81N2O6P+H)

Slide TS37 (C39H81N2O6P+H)

Slide TS38 (C39H81N2O6P+H)

C42H81O10P+NH4

Lysobisphosphatidate (10:0/0:0/26:1(17Z)/0:0), Lysobisphosphatidate (12:0/0:0/24:1(15Z)/0:0), Lysobisphosphatidate (14:0/0:0/22:1(13Z)/0:0), Lysobisphosphatidate (16:0/0:0/20:1(11Z)/0:0), Lysobisphosphatidate (18:0/0:0/18:1(6Z)/0:0), Lysobisphosphatidate (18:0/0:0/18:1(9Z)/0:0), Lysobisphosphatidate (18:0/0:0/18:1(11E)/0:0), Lysobisphosphatidate (18:0/0:0/18:1(11Z)/0:0), Lysobisphosphatidate (20:0/0:0/16:1(6Z)/0:0), Lysobisphosphatidate (20:0/0:0/16:1(9Z)/0:0), Lysobisphosphatidate (22:0/0:0/14:1(9Z)/0:0), PG(10:0/26:1(17Z)), PG(12:0/24:1(15Z)), PG(14:0/22:1(13Z)), PG(14:1(9Z)/22:0), PG(16:0/20:1(11Z)), PG(16:1(6Z)/20:0), PG(16:1(9Z)/20:0), PG(18:0/18:1(6Z)), PG(18:0/18:1(9Z)), PG(18:0/18:1(11E)), PG(18:0/18:1(11Z)), PG(18:1(6Z)/18:0), PG(18:1(9Z)/18:0), PG(18:1(11E)/18:0), PG(18:1(11Z)/18:0), PG(20:0/16:1(6Z)), PG(20:0/16:1(9Z)), PG(20:1(11Z)/16:0), PG(22:0/14:1(9Z)), PG(22:1(13Z)/14:0), PG(24:1(15Z)/12:0), PG(26:1(17Z)/10:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H81O10P+NH4)

Slide TS34 (C42H81O10P+NH4)

Slide TS35 (C42H81O10P+NH4)

Slide TS36 (C42H81O10P+NH4)

Slide TS37 (C42H81O10P+NH4)

Slide TS38 (C42H81O10P+NH4)

C42H82NO11P+Na

IPC(d18:0/18:1(9Z))

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H82NO11P+Na)

Slide TS34 (C42H82NO11P+Na)

Slide TS35 (C42H82NO11P+Na)

Slide TS36 (C42H82NO11P+Na)

Slide TS37 (C42H82NO11P+Na)

Slide TS38 (C42H82NO11P+Na)

C42H83O7P+NH4

PA(O-13:0/26:1(17Z)), PA(O-15:0/24:1(15Z)), PA(O-17:0/22:1(13Z)), PA(O-18:1(9Z)/21:0), PA(O-18:1(11Z)/21:0), PA(O-18:1(13Z)/21:0), PA(O-20:1(11Z)/19:0), PA(O-22:1(13Z)/17:0), PA(P-13:0/26:0), PA(P-15:0/24:0), PA(P-17:0/22:0), PA(P-18:0/21:0), PA(P-20:0/19:0), PA(P-22:0/17:0), PA(P-24:0/15:0), PA(P-26:0/13:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H83O7P+NH4)

Slide TS34 (C42H83O7P+NH4)

Slide TS35 (C42H83O7P+NH4)

Slide TS36 (C42H83O7P+NH4)

Slide TS37 (C42H83O7P+NH4)

Slide TS38 (C42H83O7P+NH4)

C42H84NO8P+Na

PC(4:0/30:0), PC(6:0/28:0), PC(8:0/26:0), PC(10:0/24:0), PC(12:0/22:0), PC(13:0/21:0), PC(14:0/20:0), PC(15:0/19:0), PC(16:0/18:0), PC(17:0/17:0), PC(18:0/16:0), PC(19:0/15:0), PC(20:0/14:0), PC(21:0/13:0), PC(22:0/12:0), PC(24:0/10:0), PC(26:0/8:0), PC(28:0/6:0), PC(30:0/4:0), PE(13:0/24:0), PE(15:0/22:0), PE(16:0/21:0), PE(17:0/20:0), PE(18:0/19:0), PE(19:0/18:0), PE(20:0/17:0), PE(21:0/16:0), PE(22:0/15:0), PE(24:0/13:0), PE-NMe2(15:0/20:0), PE-NMe2(20:0/15:0), PE-NMe(14:0/22:0), PE-NMe(16:0/20:0), PE-NMe(18:0/18:0), PE-NMe(20:0/16:0), PE-NMe(22:0/14:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H84NO8P+Na)

Slide TS34 (C42H84NO8P+Na)

Slide TS35 (C42H84NO8P+Na)

Slide TS36 (C42H84NO8P+Na)

Slide TS37 (C42H84NO8P+Na)

Slide TS38 (C42H84NO8P+Na)

C42H86NO7P+H

PC(O-13:0/21:0), PC(O-14:0/20:0), PC(O-15:0/19:0), PC(O-16:0/18:0), PC(O-17:0/17:0), PC(O-18:0/16:0), PC(O-20:0/14:0), PC(O-22:0/12:0), PC(O-24:0/10:0), PC(O-26:0/8:0), PC(O-28:0/6:0), PC(O-30:0/4:0), PC(o-16:0/18:0), PE(O-13:0/24:0), PE(O-15:0/22:0), PE(O-16:0/21:0), PE(O-17:0/20:0), PE(O-18:0/19:0), PE(O-20:0/17:0), PE(O-22:0/15:0), PE(O-24:0/13:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H86NO7P+H)

Slide TS34 (C42H86NO7P+H)

Slide TS35 (C42H86NO7P+H)

Slide TS36 (C42H86NO7P+H)

Slide TS37 (C42H86NO7P+H)

Slide TS38 (C42H86NO7P+H)

C43H75NO4+Na

Cer(iso-t17:0/26:6(8Z,11Z,14Z,17Z,20Z,23Z))

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C43H75NO4+Na)

Slide TS34 (C43H75NO4+Na)

Slide TS35 (C43H75NO4+Na)

Slide TS36 (C43H75NO4+Na)

Slide TS37 (C43H75NO4+Na)

Slide TS38 (C43H75NO4+Na)

C47H83NO4+Na

Cer(iso-t17:0/30:6(12Z,15Z,18Z,21Z,24Z,27Z))

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C47H83NO4+Na)

Slide TS34 (C47H83NO4+Na)

Slide TS35 (C47H83NO4+Na)

Slide TS36 (C47H83NO4+Na)

Slide TS37 (C47H83NO4+Na)

Slide TS38 (C47H83NO4+Na)

Violin Plots of Intensities of Differentially Expressed Markers

Violin plots of marker intensities (nonzero only, hotspot-clipped)